I can see Hitch's point about spacing issues for some (although it doesn't bother me in the least and I'm on a 5" reader with a larger font because of my craptastic eyes). I still don't like the look of indenting on just one side though.

What I've done in a few books that I think is a very acceptable alternative, such as for a note that should be split apart from the rest of the text, is just add a space before and after the note, and change the text to italics. Then it can stay full justified width as the rest of the book and it still stands out as it should, and you're not losing margin space at all no matter how long or short the note is. I'd much prefer this to seeing lop-sided indents.